Muscle alignment problem

Question

[majeedaasim]

I USED Muscle to create MSA which was created successfully. Also I generated the tree with PhyML from this MSA. But there appears to be a problem of cutting the taxa names to half. Instead of full names only half names appear in MSA as well as tree thereof.

The MSA looks like

VV02G00600 ---------- ---------- ---------- ---------- ----------

GM01G41530 ---------- ---------- ---------- ---------- ----------

OSINDICA_0 ---------- ---------- ---------- ---------- ----------

ZM01G03180 ---------- ---------- ---------- ---------- ----------


Tw_Wn_DN14 ---------- ---------- ---------- ---------- ----------

Tw_Wn_DN11 ---------- ---------- ---------- ---------- ----------

Tw_Wn_DN92 ---------- ---------- ---------- ---------- ----------

Tw_Wn_DN12 ---------- ---------- ---------- ---------- ----------

However the full names of the sequences look like

VV02G00600_sed_34_GS

Tw_Wn_DN14_c0_i2_i6

etc.

Also for Arabidopsis thaliana, the name appears as Arabidopsi

This is happening for every name.

How to solve it.

Thanks

[GenoMax]

Welcome to the world of phylogenetics. Many standard phylogenetic programs limit the names to 10 characters. You would need to ensure that you rename your sequences so that first 10 characters make sense. If not, use a different program.

Answer 1

[Robert W Link]

Your answer looks like the MSA is in Phylip format, which will truncate the sequence header to the first 10 characters.

If you need to keep in Phylip format, you should opt for a relaxed Phylip format, which cannot be performed in MUSCLE, unfortunately...

However, you can output your MSA in a FASTA format and use http://aligner.azurewebsites.net/ to convert it from FASTA to relaxed Phylip.